OpenMS  2.8.0
Classes | Public Member Functions | Private Member Functions | List of all members
AbsoluteQuantitationStandards Class Reference

AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations. More...

#include <OpenMS/METADATA/AbsoluteQuantitationStandards.h>

Classes

struct  featureConcentration
 Structure to hold a single component and its corresponding known concentration. More...
 
struct  runConcentration
 Structure to map runs to components to known concentrations. More...
 

Public Member Functions

 AbsoluteQuantitationStandards ()=default
 Constructor. More...
 
 ~AbsoluteQuantitationStandards ()=default
 Destructor. More...
 
void mapComponentsToConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, std::map< String, std::vector< AbsoluteQuantitationStandards::featureConcentration >> &components_to_concentrations) const
 Method to map runs to components to known concentrations. More...
 
void getComponentFeatureConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, const String &component_name, std::vector< AbsoluteQuantitationStandards::featureConcentration > &feature_concentrations) const
 Get the feature concentrations from a single component. More...
 

Private Member Functions

bool findComponentFeature_ (const FeatureMap &feature_map, const String &component_name, Feature &feature_found) const
 Finds a feature for a given component name. More...
 

Detailed Description

AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations.

A mapping between a run, the components in the run, and the actual concentration of the components in the run are required to build a calibration curve that is required for absolute quantitation.


Class Documentation

◆ OpenMS::AbsoluteQuantitationStandards::featureConcentration

struct OpenMS::AbsoluteQuantitationStandards::featureConcentration

Structure to hold a single component and its corresponding known concentration.

Collaboration diagram for AbsoluteQuantitationStandards::featureConcentration:
[legend]
Class Members
double actual_concentration
String concentration_units
double dilution_factor
Feature feature
double IS_actual_concentration
Feature IS_feature

◆ OpenMS::AbsoluteQuantitationStandards::runConcentration

struct OpenMS::AbsoluteQuantitationStandards::runConcentration

Structure to map runs to components to known concentrations.

Collaboration diagram for AbsoluteQuantitationStandards::runConcentration:
[legend]
Class Members
double actual_concentration
String component_name
String concentration_units
double dilution_factor
double IS_actual_concentration
String IS_component_name
String sample_name

Constructor & Destructor Documentation

◆ AbsoluteQuantitationStandards()

Constructor.

◆ ~AbsoluteQuantitationStandards()

Destructor.

Member Function Documentation

◆ findComponentFeature_()

bool findComponentFeature_ ( const FeatureMap feature_map,
const String component_name,
Feature feature_found 
) const
private

Finds a feature for a given component name.

Parameters
[in]feature_mapThe container of features.
[in]component_nameThe feature must have this name as its "native_id".
[out]feature_foundIf found, the feature is saved in this parameter.

◆ getComponentFeatureConcentrations()

void getComponentFeatureConcentrations ( const std::vector< AbsoluteQuantitationStandards::runConcentration > &  run_concentrations,
const std::vector< FeatureMap > &  feature_maps,
const String component_name,
std::vector< AbsoluteQuantitationStandards::featureConcentration > &  feature_concentrations 
) const

Get the feature concentrations from a single component.

This method internally calls `mapComponentsToConcentrations()`, but takes in consideration only those elements of `run_concentrations` that have the passed `component_name`.

Warning
The method checks for the FeatureMaps' sample names with FeatureMap::getPrimaryMSRunPath()
Parameters
[in]run_concentrationsA list of runConcentration structs (e.g., from file upload).
[in]feature_mapsThe method maps to these features.
[in]component_nameOnly runConcentration with this name will be considered.
[out]feature_concentrationsThe list of feature concentrations found.

◆ mapComponentsToConcentrations()

void mapComponentsToConcentrations ( const std::vector< AbsoluteQuantitationStandards::runConcentration > &  run_concentrations,
const std::vector< FeatureMap > &  feature_maps,
std::map< String, std::vector< AbsoluteQuantitationStandards::featureConcentration >> &  components_to_concentrations 
) const

Method to map runs to components to known concentrations.

Warning
The method checks for the FeatureMaps' sample names with FeatureMap::getPrimaryMSRunPath()
Parameters
[in]run_concentrationsA list of runConcentration structs (e.g., from file upload).
[in]feature_mapsThe method maps to these features.
[out]components_to_concentrationsA map that links run data to feature data.